htsjdk.samtools

Class SAMRecordSetBuilder

java.lang.Object

htsjdk.samtools.SAMRecordSetBuilder

All Implemented Interfaces:

java.lang.Iterable<SAMRecord>

public class SAMRecordSetBuilder
extends java.lang.Object
implements java.lang.Iterable<SAMRecord>

Factory class for creating SAMRecords for testing purposes. Various methods can be called to add new SAM records (or pairs of records) to a list which can then be returned at any point. The records must reference human chromosomes (excluding randoms etc.).

Although this is a class for testing, it is in the src tree because it is included in the sam jarfile.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_CHROMOSOME_LENGTH
static DuplicateScoringStrategy.ScoringStrategy	DEFAULT_DUPLICATE_SCORING_STRATEGY

Constructor Summary

Constructors

Constructor and Description
SAMRecordSetBuilder() Constructs a new SAMRecordSetBuilder with all the data needed to keep the records sorted in coordinate order.
SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder) Construct a new SAMRecordSetBuilder.
SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup)
SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup, int defaultChromosomeLength)
SAMRecordSetBuilder(boolean sortForMe, SAMFileHeader.SortOrder sortOrder, boolean addReadGroup, int defaultChromosomeLength, DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)

Method Summary

Modifier and Type	Method and Description
SAMRecord	addFrag(java.lang.String name, int contig, int start, boolean negativeStrand) Adds a skeletal fragment (non-PE) record to the set using the provided contig start and strand information.
SAMRecord	addFrag(java.lang.String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, java.lang.String cigar, java.lang.String qualityString, int defaultQuality) Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
SAMRecord	addFrag(java.lang.String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, java.lang.String cigar, java.lang.String qualityString, int defaultQuality, boolean isSecondary) Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
SAMRecord	addFrag(java.lang.String name, int contig, int start, boolean negativeStrand, boolean recordUnmapped, java.lang.String cigar, java.lang.String qualityString, int defaultQuality, boolean isSecondary, boolean isSupplementary) Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.
void	addPair(java.lang.String name, int contig, int start1, int start2) Adds a skeletal pair of records to the set using the provided contig starts.
java.util.List<SAMRecord>	addPair(java.lang.String name, int contig, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, java.lang.String cigar1, java.lang.String cigar2, boolean strand1, boolean strand2, boolean record1NonPrimary, boolean record2NonPrimary, int defaultQuality) Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
java.util.List<SAMRecord>	addPair(java.lang.String name, int contig, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, java.lang.String cigar1, java.lang.String cigar2, boolean strand1, boolean strand2, int defaultQuality) Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
java.util.List<SAMRecord>	addPair(java.lang.String name, int contig1, int contig2, int start1, int start2, boolean record1Unmapped, boolean record2Unmapped, java.lang.String cigar1, java.lang.String cigar2, boolean strand1, boolean strand2, boolean record1NonPrimary, boolean record2NonPrimary, int defaultQuality) Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts.
void	addRecord(SAMRecord record) The record should already have the DS and MC tags computed
void	addUnmappedFragment(java.lang.String name) Adds an unmapped fragment read to the builder.
void	addUnmappedPair(java.lang.String name) Adds a pair with both ends unmapped to the builder.
SAMFileHeader	getHeader()
java.util.Collection<SAMRecord>	getRecords() Returns the accumulated list of sam records.
SamReader	getSamReader() Creates samFileReader from the data in instance of this class
CloseableIterator<SAMRecord>	iterator() Returns a CloseableIterator over the collection of SAMRecords.
void	setHeader(SAMFileHeader header)
void	setProgramRecord(SAMProgramRecord programRecord) Adds the given program record to the header, and assigns the PG tag to any SAMRecords created after it has been added.
void	setRandomSeed(long seed) Set the seed of the random number generator for cases in which repeatable result is desired.
void	setReadGroup(SAMReadGroupRecord readGroup)
void	setReadLength(int readLength)
void	setUnmappedHasBasesAndQualities(boolean value)
void	setUseNmFlag(boolean useNmFlag)
int	size()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

DEFAULT_CHROMOSOME_LENGTH

public static final int DEFAULT_CHROMOSOME_LENGTH

See Also:

Constant Field Values

DEFAULT_DUPLICATE_SCORING_STRATEGY

public static final DuplicateScoringStrategy.ScoringStrategy DEFAULT_DUPLICATE_SCORING_STRATEGY

Constructor Detail

SAMRecordSetBuilder

public SAMRecordSetBuilder()

Constructs a new SAMRecordSetBuilder with all the data needed to keep the records sorted in coordinate order.

SAMRecordSetBuilder

public SAMRecordSetBuilder(boolean sortForMe,
                           SAMFileHeader.SortOrder sortOrder)

Construct a new SAMRecordSetBuilder.

Parameters:

sortOrder - If sortForMe, defines the sort order.

sortForMe - If true, keep the records created in sorted order.

SAMRecordSetBuilder

public SAMRecordSetBuilder(boolean sortForMe,
                           SAMFileHeader.SortOrder sortOrder,
                           boolean addReadGroup)

SAMRecordSetBuilder

public SAMRecordSetBuilder(boolean sortForMe,
                           SAMFileHeader.SortOrder sortOrder,
                           boolean addReadGroup,
                           int defaultChromosomeLength)

SAMRecordSetBuilder

public SAMRecordSetBuilder(boolean sortForMe,
                           SAMFileHeader.SortOrder sortOrder,
                           boolean addReadGroup,
                           int defaultChromosomeLength,
                           DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)

Method Detail

setUnmappedHasBasesAndQualities

public void setUnmappedHasBasesAndQualities(boolean value)

size

public int size()

setRandomSeed

public void setRandomSeed(long seed)

Set the seed of the random number generator for cases in which repeatable result is desired.

Parameters:

seed -

setProgramRecord

public void setProgramRecord(SAMProgramRecord programRecord)

Adds the given program record to the header, and assigns the PG tag to any SAMRecords created after it has been added. May be called multiple times in order to assign different PG IDs to different SAMRecords. programRecord may be null to stop assignment of PG tag. It is up to the caller to ensure that program record IDs do not collide.

setUseNmFlag

public void setUseNmFlag(boolean useNmFlag)

setReadGroup

public void setReadGroup(SAMReadGroupRecord readGroup)

getRecords

public java.util.Collection<SAMRecord> getRecords()

Returns the accumulated list of sam records.

setHeader

public void setHeader(SAMFileHeader header)

addRecord

public void addRecord(SAMRecord record)

The record should already have the DS and MC tags computed

iterator

public CloseableIterator<SAMRecord> iterator()

Returns a CloseableIterator over the collection of SAMRecords.

Specified by:

iterator in interface java.lang.Iterable<SAMRecord>

addFrag

public SAMRecord addFrag(java.lang.String name,
                         int contig,
                         int start,
                         boolean negativeStrand)

Adds a skeletal fragment (non-PE) record to the set using the provided contig start and strand information.

addFrag

public SAMRecord addFrag(java.lang.String name,
                         int contig,
                         int start,
                         boolean negativeStrand,
                         boolean recordUnmapped,
                         java.lang.String cigar,
                         java.lang.String qualityString,
                         int defaultQuality)
                  throws SAMException

Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.

Throws:

SAMException

addFrag

public SAMRecord addFrag(java.lang.String name,
                         int contig,
                         int start,
                         boolean negativeStrand,
                         boolean recordUnmapped,
                         java.lang.String cigar,
                         java.lang.String qualityString,
                         int defaultQuality,
                         boolean isSecondary)
                  throws SAMException

Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.

Throws:

SAMException

addFrag

public SAMRecord addFrag(java.lang.String name,
                         int contig,
                         int start,
                         boolean negativeStrand,
                         boolean recordUnmapped,
                         java.lang.String cigar,
                         java.lang.String qualityString,
                         int defaultQuality,
                         boolean isSecondary,
                         boolean isSupplementary)
                  throws SAMException

Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand, cigar string, quality string or default quality score.

Throws:

SAMException

addUnmappedFragment

public void addUnmappedFragment(java.lang.String name)

Adds an unmapped fragment read to the builder.

addPair

public void addPair(java.lang.String name,
                    int contig,
                    int start1,
                    int start2)

Adds a skeletal pair of records to the set using the provided contig starts. The pair is assumed to be a well formed pair sitting on a single contig.

addPair

public java.util.List<SAMRecord> addPair(java.lang.String name,
                                         int contig,
                                         int start1,
                                         int start2,
                                         boolean record1Unmapped,
                                         boolean record2Unmapped,
                                         java.lang.String cigar1,
                                         java.lang.String cigar2,
                                         boolean strand1,
                                         boolean strand2,
                                         int defaultQuality)

Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts. The pair is assumed to be a well formed pair sitting on a single contig.

addPair

public java.util.List<SAMRecord> addPair(java.lang.String name,
                                         int contig1,
                                         int contig2,
                                         int start1,
                                         int start2,
                                         boolean record1Unmapped,
                                         boolean record2Unmapped,
                                         java.lang.String cigar1,
                                         java.lang.String cigar2,
                                         boolean strand1,
                                         boolean strand2,
                                         boolean record1NonPrimary,
                                         boolean record2NonPrimary,
                                         int defaultQuality)

Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts. The pair is assumed to be a well formed pair sitting on a single contig.

addPair

public java.util.List<SAMRecord> addPair(java.lang.String name,
                                         int contig,
                                         int start1,
                                         int start2,
                                         boolean record1Unmapped,
                                         boolean record2Unmapped,
                                         java.lang.String cigar1,
                                         java.lang.String cigar2,
                                         boolean strand1,
                                         boolean strand2,
                                         boolean record1NonPrimary,
                                         boolean record2NonPrimary,
                                         int defaultQuality)

Adds a pair of records (mapped or unmmapped) to the set using the provided contig starts. The pair is assumed to be a well formed pair sitting on a single contig.

addUnmappedPair

public void addUnmappedPair(java.lang.String name)

Adds a pair with both ends unmapped to the builder.

getSamReader

public SamReader getSamReader()

Creates samFileReader from the data in instance of this class

Returns:

SamReader

getHeader

public SAMFileHeader getHeader()

setReadLength

public void setReadLength(int readLength)